The Ontology Lookup Service (OLS) is now indexing dense embeddings for ontology terms constructed from term labels, synonyms, and descriptions using LLMs. I maintain a Python client library for the OLS (ols-client) and was recently asked to implement a wrapper to the OLS’s API endpoint that exposes these embeddings.

I have finally opened a Posts section on my website! Every post should now automatically get a DOI.

The American Society for Microbiology (ASM) has earned recognition in Crossref’s Participation Reports for its exceptional metadata coverage among large publishing members––an achievement built on intentional change, technical investment, and collaborative work.

I recently gave a 30-minute talk at the Librarian Futures Virtual Summit, and for the topic of "AI-powered search," I decided to play devil's advocate.

In Archie Carr’s encyclopedic “Handbook of Turtles: The Turtles of the United States, Canada, and Baja California”, first published in 1952, he quotes favorably and at length the observations of “Mrs. Knowlton” on the behavior of wood turtles (Clemmys insculpta) and box turtles (Terrapene carolina). The source given in the references is: Knowlton, Josphine Gibson.

Or how I’m slowly coming to my senses.

Adam Mastroianni’s blog Experimental History is consistently fascinating. In a recent article on whether conversations end when people want them to, he makes this point, very much in passing: This is a brilliant insight, and it explains so much about what’s wrong with journal articles. When you’re balancing all six requirements, how are you ever going to write something that people are going to actually enjoy reading?

Natalia Calderón, DR © Grabado Xalapa, Veracruz. 2023 Parte de la colección “Gráfica” Sitio de la autora Esta es una reproducción digital, con fines de divulgación, de una obra original proporcionada por su autor o propietario. Todos los derechos están reservados por la artista.

This week’s recap highlights Variant-EFFECTS for rewriting regulatory DNA to dissect and reprogram gene expression, zero-shot evaluation revealing the limitations of single-cell foundation models, EcoWeaver for large-scale prediction of gene functional associations from coevolutionary signals, and how assemblies of long-read metagenomes suffer from diverse errors.

There’s a moment—somewhere in the quiet space between hypothesis and imagination—when science fiction stops feeling like fiction at all. I remember it clearly. We were outlining the premise of On the Wings of a Pig , building the scaffolding of a story that spanned lightyears and lifetimes.

by Sofia Baroncini, Constanze Buyken, Judit Garzón Rodríguez, Ian Kisil Marino, Sarah Oberbichler, Cindarella Petz The 2025 Digital Humanities Conference, held this year in Lisbon under the theme “Building Access and Accessibility: Open Science to All Citizens”, brought together a global community of researchers, developers, and practitioners to reflect on the role of openness, inclusivity, … „From Access to Ethics: Data Discussions at the